Trait: triple-negative breast cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005537
Description An invasive breast carcinoma which is negative for expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). [NCIT: P378]
Trait category
Cancer
Synonyms 5 synonyms
  • triple-receptor negative breast cancer
  • Triple-Negative Breast Carcinoma
  • triple-negative breast cancer
  • TN breast cancer
  • triple-negative breast carcinoma
Mapped term(s) 7 mapped terms
  • DOID:0060081
  • MESH:D064726
  • UMLS:C3539878
  • SCTID:706970001
  • MONDO:0005494
  • NCIT:C71732
  • SNOMEDCT:706970001

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000216 PRS330_TN PGP000088
Zhang H et al. Nat Genet (2020)
Breast cancer intrinsic-like subtype (triple negative) triple-negative breast cancer 330 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000216/ScoringFiles/PGS000216.txt.gz

PGS Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance Metric ID
(PPM ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000661 PGS000216 (PRS330_TN) PSS000363 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (triple negative) OR: 1.65[1.57, 1.73] AUROC: 0.6358

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000363 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (5) triple-negative ( ER-, PR-, HER2-). 
[
  • 2,006 cases
  • , 20,815 controls
]
,
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data